Light Sheet Tomography (LST) for <i>in situ</i> imaging of plant roots

The production of crops capable of efficient nutrient use is essential for addressing the problem of global food security. The ability of a plant's root system to interact with the soil micro-environment determines how effectively it can extract water and nutrients. In order to assess this ability and develop the fast and cost effective phenotyping techniques which are needed to establish efficient root systems, in situ imaging in soil is required. To date this has not been possible due to the high density of scatterers and absorbers in soil or because other growth substrates do not sufficiently model the heterogeneity of a soil's microenvironment. We present here a new form of light sheet imaging with novel transparent soil containing refractive index matched particles. This imaging method does not rely on fluorescence, but relies solely on scattering from root material. We term this form of imaging Light Sheet Tomography (LST). We have tested LST on a range of materials and plant roots in transparent soil and gel. Due to the low density of root structures, i.e. relatively large spaces between adjacent roots, long-term monitoring of lettuce root development in situ with subsequent quantitative analysis was achieved

Publishing and sharing multi-dimensional image data with OMERO

Imaging data are used in the life and biomedical sciences to measure the molecular and structural composition and dynamics of cells, tissues, and organisms. Datasets range in size from megabytes to terabytes and usually contain a combination of binary pixel data and metadata that describe the acquisition process and any derived results. The OMERO image data management platform allows users to securely share image datasets according to specific permissions levels: data can be held privately, shared with a set of colleagues, or made available via a public URL. Users control access by assigning data to specific Groups with defined membership and access rights. OMERO’s Permission system supports simple data sharing in a lab, collaborative data analysis, and even teaching environments. OMERO software is open source and released by the OME Consortium at www.openmicroscopy.org

Metadata management for high content screening in OMERO

High content screening (HCS) experiments create a classic data management challenge—multiple, large sets of heterogeneous structured and unstructured data, that must be integrated and linked to produce a set of “final” results. These different data include images, reagents, protocols, analytic output, and phenotypes, all of which must be stored, linked and made accessible for users, scientists, collaborators and where appropriate the wider community. The OME Consortium has built several open source tools for managing, linking and sharing these different types of data. The OME Data Model is a metadata specification that supports the image data and metadata recorded in HCS experiments. Bio-Formats is a Java library that reads recorded image data and metadata and includes support for several HCS screening systems. OMERO is an enterprise data management application that integrates image data, experimental and analytic metadata and makes them accessible for visualization, mining, sharing and downstream analysis. We discuss how Bio-Formats and OMERO handle these different data types, and how they can be used to integrate, link and share HCS experiments in facilities and public data repositories. OME specifications and software are open source and are available at https://www.openmicroscopy.org

Epistemologie der Erziehungswissenschaft: Dilemmas, Fragen, mögliche Lösungen

U radu se polazi od tvrdnje da su epistemološke karakteristike temeljne odrednice znanstvenog digniteta znanosti. Na osnovi kritičke analize epistemoloških karakteristika pedagogije upozorava se na upitnost njezina znanstvenog digniteta. Navedena se tvrdnja obrazlaže odgovorima na nekoliko pitanja: Je li razina razvijenosti suvremenog društva nametnula potrebu redefiniranja semantičkog određenja osnovnih pojmova i pedagogije same? Može li se pedagogija koja desetljećima nije promijenila svoj osnovni teorijski, epistemološko-metodologijski koncept, smatrati suvremenom? Ima li Hrvatska suvremenu pedagogiju ili je riječ o tradicionalnoj (zastarjeloj) pedagogiji? Što je osnovna funkcija pedagogije? Je li pedagogija znanost o odgoju, znanost o odgoju i obrazovanju ili znanost o osposobljavanju ljudi? Jesu li cilj i zadaci pedagogijske znanosti jednoznačno određeni? Na kraju se navode moguća rješenja. Predlažu se nova suvremena jednoznačna semantička određenja temeljnih pojmova i s tog se aspekta utvrđuje osnovna funkcija pedagogije i kao znanstvene i kao praktične discipline, kao teorije osposobljavanja.The argumentation presented in the paper starts from the premise that epistemological characteristics are the elements that science builds its scientific dignity on. A critical analysis of the epistemological characteristics of pedagogy has led the author to question its scientific dignity. The doubts stated in the paper are raised by several questions. Is the level of development of the modern society forcing us to redefine the semantic components of basic pedagogical terms and pedagogy itself? Can pedagogy, which has not changed its basic theoretical, epistemological and methodological concept for decades, really be termed contemporary? Is pedagogy in Croatia contemporary or do we still practice the traditional (and outdated) form of pedagogy? What is the main function of pedagogy? Is pedagogy the science of education, the science of education and development, or the science of human resources development? Are the goals and tasks of pedagogy as a science unambiguously set? Finally, the author suggests possible answers, advocating new, modern and unambiguous semantic definitions of the basic terms, thus determining the primary function of pedagogy as both scientific and practical discipline – a human resources development theory.Den Ausgangspunkt dieser Arbeit bildet die These, dass epistemologische Charakteristiken die wissenschaftliche Dignität jeder Wissenschaft begründen. Anhand einer kritischen Analyse von epistemologischen Charakteristiken der Erziehungswissenschaft wird auf die Fragwürdigkeit ihrer wissenschaftlichen Dignität hingewiesen, Die angeführte Behauptung wird durch Antworten auf einige Fragen erklärt: Macht die Entwicklungsebene der modernen Gesellschaft eine Redefinition der semantischen Bestimmungen pädagogischer Grundbegriffe und der Pädagogik selbst erforderlichß Kann die Erziehungswissenschaft, die seit Jahrzehnten ihr theoretisches, epistemologisch – methodologisches Grundkonzept nicht geändert hat, als modern gelten? Hat Kroatien eine moderne Erziehungswissenschaft oder ob es um eine traditionelle (veraltete) Pädagogik handelt? Was ist die Grundaufgabe der Pädagogik? Ist die Pädagogik eine Wissenschaft über die Erziehung, Wissenschaft über die Erziehung und Bildung oder Wissenschaft über die Befähigung der Menschen? Lassen sich das Ziel und die Aufgaben der Erziehungswissenschaft eindeutig bestimmen? Am Ende werden mögliche Lösungen angeführt. Vorgeschlagen werden neue moderne eindeutige semantische Bestimmungen der pädagogischen Grundbegriffe und von diesem Standpunkt aus Grundaufgaben der Pädagogik sowohl als wissenschaftlicher als auch praktischer Disziplin sowie einer Befähigungstheorie festgelegt

Effects of spin-orbit coupling and many-body interactions on the electronic structure of Sr₂RuO₄

The aim of the project is to investigate the effects of spin-orbit coupling and many-body interactions on the band structure of the single-layered strontium ruthenate Sr₂RuO₄. This material belongs to the large family of strongly correlated electron systems in which electron-electron interaction plays a crucial role in determining the macroscopic properties. The experimental method used for this purpose is Angular Resolved Photoemission Spectroscopy (ARPES), which probes the single-particle spectral function and allows direct measurements of the quasi-particle band structure. The analysis is based on comparison of experimental data with electronic structure calculations. Typical methods for the band structure calculations including density functional theory (DFT) in the local density approximation (LDA) and tight-binding calculations (TB) are one-electron approximations and do not give insight into many-body interactions. However, comparing the measured band structures with calculated ones allows estimating the strength of the interactions in the considered system. In Chapter 1 the earlier work on Sr₂RuO₄, which is relevant to this project is presented. This chapter is an introduction to the data analysis and discussion of the results. In Chapter 2 we describe the experimental setup, theoretical principles of the measurement and summarize important improvements made during this project. In Chapter 3 we give a brief introduction into density functional theory and describe methods used within DFT to calculate the band structure. We further give a brief description of a tight binding model for Sr₂RuO₄. The bulk of this chapter is devoted to present the effects of spin-orbit coupling on the band structure of Sr₂RuO₄. In particular, we use a tight binding model to simulate the anisotropy of the Zeeman splitting found experimentally. In Chapter 4 we present the ARPES results, their analysis and discussion. A particular focus is placed on the discussion of the surface layer Fermi surface topology and on the discovery of strong momentum dependence of the mass renormalization factors of the bulk β and γ bands

Spin-orbit coupling and k-dependent Zeeman splitting in strontium ruthenate

We compare the relativistic LDA Fermi surface of Sr(2)RuO(4) to direct experimental evidence of spin-orbit coupling from de Haas-van Alphen experiments. The k-dependence of the Zeeman splitting at the Fermi surface is modelled with a range of tight binding models of the quasi-particle bands. Only a very restricted class of parameters are consistent with evidence from the de Haas-van Alphen experiments for a strong k-dependent Zeeman splitting on the alpha Fermi surface sheet. The bare LDA bands do not lead to such a strong k-dependent Zeeman splitting on this sheet, and this suggests that additional charge transfer takes place as suggested by DMFT calculations. We conclude that the overall scale of the spin-orbit coupling must be at least as large as the several hundred kelvin deduced in previous work, and that this must call into question any theory postulating rotation of the triplet d-vector at small magnetic fields

Media 1: Light Sheet Tomography (LST) for in situ imaging of plant roots

Originally published in Optics Express on 15 July 2013 (oe-21-14-16239